155 lines
4.8 KiB
C++
155 lines
4.8 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "omp_compat.h"
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#include "npair_full_multi_omp.h"
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#include "npair_omp.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "molecule.h"
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#include "domain.h"
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#include "my_page.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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binned neighbor list construction for all neighbors
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multi stencil is icollection-jcollection dependent
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every neighbor pair appears in list of both atoms i and j
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------------------------------------------------------------------------- */
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void NPairFullMultiOmp::build(NeighList *list)
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{
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const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
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const int molecular = atom->molecular;
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const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
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NPAIR_OMP_INIT;
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#if defined(_OPENMP)
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#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
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#endif
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NPAIR_OMP_SETUP(nlocal);
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int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom;
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tagint tagprev;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighptr,*s;
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int js;
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// loop over each atom, storing neighbors
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int *collection = neighbor->collection;
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double **x = atom->x;
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int *type = atom->type;
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int *mask = atom->mask;
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tagint *tag = atom->tag;
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tagint *molecule = atom->molecule;
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tagint **special = atom->special;
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int **nspecial = atom->nspecial;
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int *molindex = atom->molindex;
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int *molatom = atom->molatom;
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Molecule **onemols = atom->avec->onemols;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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// each thread has its own page allocator
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MyPage<int> &ipage = list->ipage[tid];
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ipage.reset();
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for (i = ifrom; i < ito; i++) {
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n = 0;
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neighptr = ipage.vget();
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itype = type[i];
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icollection = collection[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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if (moltemplate) {
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imol = molindex[i];
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iatom = molatom[i];
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tagprev = tag[i] - iatom - 1;
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}
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ibin = atom2bin[i];
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// loop through stencils for all collections
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for (jcollection = 0; jcollection < ncollections; jcollection++) {
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// if same collection use own bin
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if (icollection == jcollection) jbin = ibin;
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else jbin = coord2bin(x[i], jcollection);
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// loop over all atoms in surrounding bins in stencil including self
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// skip i = j
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// use full stencil for all collection combinations
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s = stencil_multi[icollection][jcollection];
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ns = nstencil_multi[icollection][jcollection];
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for (k = 0; k < ns; k++) {
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js = binhead_multi[jcollection][jbin + s[k]];
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for (j = js; j >= 0; j = bins[j]) {
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if (i == j) continue;
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jtype = type[j];
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular != Atom::ATOMIC) {
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if (!moltemplate)
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which = find_special(special[i],nspecial[i],tag[j]);
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else if (imol >= 0)
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which = find_special(onemols[imol]->special[iatom],
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onemols[imol]->nspecial[iatom],
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tag[j]-tagprev);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (domain->minimum_image_check(delx,dely,delz))
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neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
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} else neighptr[n++] = j;
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}
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}
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}
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}
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ilist[i] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage.vgot(n);
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if (ipage.status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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NPAIR_OMP_CLOSE;
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list->inum = nlocal;
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list->gnum = 0;
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}
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